..Overall, our analysis demonstrates the commonalities underpinning a variety of pathologies as seen in both hypercoagulability and hypofibrinolysis, and offers opportunities for both diagnostics and therapies. ..

..This needs to be acquired in cells that contain the relevant proteins, and we highlight an experimental system for simultaneous genome-wide assessment of carrier-mediated uptake in a eukaryotic cell (yeast)...

Douglas B KellSchool of Chemistry and The Manchester Centre for Integrative Systems Biology, The Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UKIUBMB Life 59:689-95. 2007

..This kind of architecture permits the distributed yet integrated goal of an evolving 'digital human' model to be realized...

The markup is the model: reasoning about systems biology models in the Semantic Web era

..Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization...

..A variety of systems biology approaches, that I summarise, can predict both the mechanisms involved in these cell death pathways and the optimal sites of action for nutritional or pharmacological interventions...

Systems biology, metabolic modelling and metabolomics in drug discovery and development

Theodor Bücher Lecture. Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB conference in Budapest

..These metrics show that the landscape is rugged, with many local optima, and that this arises from a combination of experimental variation and the natural structural properties of the oligonucleotides...

Predictive models for population performance on real biological fitness landscapes

William RoweFaculty of Life Sciences, The University of Manchester, Michael Smith Building, UKBioinformatics 26:2145-52. 2010

..Here, we use the method for the first time to simulate a biological fitness landscape based on experimental evaluation...

..It is also suitable for large-scale mining, since multiple reactions and their kinetic parameters can be specified in a single search request, rather than one reaction at a time, which is unsuitable given the size of genome-scale models...

Steve O'HaganSchool of Chemistry, The University of Manchester, Manchester, UKPLoS ONE 7:e48862. 2012

..The non-proprietary code that we have used is made freely available (via Supplementary information)...

A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

Makoto MiwaThe National Centre for Text Mining and School of Computer Science and School of Chemistry and the Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UKBioinformatics 29:i44-52. 2013

..These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge...

Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures

..The data were used to indicate possible biomarkers of pre-eclampsia and showed both the instruments and XCMS to be applicable to the reproducible and valid detection of disease biomarkers present in serum...

Information-theoretic sensitivity analysis: a general method for credit assignment in complex networks

..Evolutionary searches provide a powerful and general approach to the discovery of new combinations of pharmacological agents with therapeutic indices potentially greater than those of single drugs...

..maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool...

..The best aptameric sequence was void of the set of four guanine repeats typifying thrombin aptamers and, thus, highlights the benefits of evolution performed in an environment closely mimicking the final diagnostic application...

Convergent evolution to an aptamer observed in small populations on DNA microarrays

..To provide definitive identification metabolite-specific mass spectral libraries for UPLC-MS and GC-MS have been constructed for 1,065 commercially available authentic standards. The MMD data are available at http://dbkgroup.org/MMD/...

A systematic survey of the response of a model NF-κB signalling pathway to TNFα stimulation

..A variety of computational methods served to explain the basis for the improvement. This closed-loop optimization strategy is a generic and powerful approach for the optimization of any analytical instrumentation...

Something from nothing: bridging the gap between constraint-based and kinetic modelling

..By adding meaning to text, these techniques produce a more structured analysis of textual knowledge than simple word searches, and can provide powerful tools for the production and analysis of systems biology models...

Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae

..In this way, the encoding of cellular and higher-order activities by genes is seen as directly analogous to computer programs. This analogy is of utility in biological genetics and in problems of genotype-phenotype mapping...

Synergistic control of oscillations in the NF-kappaB signalling pathway

A E C IhekwabaSchool of Chemistry, The University of Manchester, UKSyst Biol (Stevenage) 152:153-60. 2005

....

Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era

..Many fields are data-rich but hypothesis-poor. Here, computational methods of data analysis, which may be automated, provide the means of generating novel hypotheses, especially in the post-genomic era...

..By using appropriate clustering and machine learning techniques, the latter based on genetic programming, we show that metabolic footprinting is an effective method to classify 'unknown' mutants by genetic defect...

..We believe this approach will aid in the Hazard Analysis Critical Control Point process for the assessment of the microbiological safety of food at the production, processing, manufacturing, packaging, and storage levels...

Metabolomic biomarkers: search, discovery and validation

Douglas B KellExpert Rev Mol Diagn 7:329-33. 2007

Discrimination of modes of action of antifungal substances by use of metabolic footprinting